%0 Journal Article %J Nature %D 2004 %T Genome sequence of the Brown Norway rat yields insights into mammalian evolution. %A Gibbs, Richard A %A Weinstock, George M %A Metzker, Michael L %A Muzny, Donna M %A Sodergren, Erica J %A Scherer, Steven %A Scott, Graham %A Steffen, David %A Worley, Kim C %A Burch, Paula E %A Okwuonu, Geoffrey %A Hines, Sandra %A Lewis, Lora %A DeRamo, Christine %A Delgado, Oliver %A Dugan-Rocha, Shannon %A Miner, George %A Morgan, Margaret %A Hawes, Alicia %A Gill, Rachel %A Holt, Robert A %A Adams, Mark D %A Amanatides, Peter G %A Baden-Tillson, Holly %A Barnstead, Mary %A Chin, Soo %A Evans, Cheryl A %A Ferriera, Steve %A Fosler, Carl %A Glodek, Anna %A Gu, Zhiping %A Jennings, Don %A Kraft, Cheryl L %A Nguyen, Trixie %A Pfannkoch, Cynthia M %A Sitter, Cynthia %A Sutton, Granger G %A Venter, J Craig %A Woodage, Trevor %A Smith, Douglas %A Lee, Hong-Mei %A Gustafson, Erik %A Cahill, Patrick %A Kana, Arnold %A Doucette-Stamm, Lynn %A Weinstock, Keith %A Fechtel, Kim %A Weiss, Robert B %A Dunn, Diane M %A Green, Eric D %A Blakesley, Robert W %A Bouffard, Gerard G %A De Jong, Pieter J %A Osoegawa, Kazutoyo %A Zhu, Baoli %A Marra, Marco %A Schein, Jacqueline %A Bosdet, Ian %A Fjell, Chris %A Jones, Steven %A Krzywinski, Martin %A Mathewson, Carrie %A Siddiqui, Asim %A Wye, Natasja %A McPherson, John %A Zhao, Shaying %A Fraser, Claire M %A Shetty, Jyoti %A Shatsman, Sofiya %A Geer, Keita %A Chen, Yixin %A Abramzon, Sofyia %A Nierman, William C %A Havlak, Paul H %A Chen, Rui %A Durbin, K James %A Simons, Rain %A Ren, Yanru %A Song, Xing-Zhi %A Li, Bingshan %A Liu, Yue %A Qin, Xiang %A Cawley, Simon %A Worley, Kim C %A Cooney, A J %A D'Souza, Lisa M %A Martin, Kirt %A Wu, Jia Qian %A Gonzalez-Garay, Manuel L %A Jackson, Andrew R %A Kalafus, Kenneth J %A McLeod, Michael P %A Milosavljevic, Aleksandar %A Virk, Davinder %A Volkov, Andrei %A Wheeler, David A %A Zhang, Zhengdong %A Bailey, Jeffrey A %A Eichler, Evan E %A Tuzun, Eray %A Birney, Ewan %A Mongin, Emmanuel %A Ureta-Vidal, Abel %A Woodwark, Cara %A Zdobnov, Evgeny %A Bork, Peer %A Suyama, Mikita %A Torrents, David %A Alexandersson, Marina %A Trask, Barbara J %A Young, Janet M %A Huang, Hui %A Wang, Huajun %A Xing, Heming %A Daniels, Sue %A Gietzen, Darryl %A Schmidt, Jeanette %A Stevens, Kristian %A Vitt, Ursula %A Wingrove, Jim %A Camara, Francisco %A Mar Albà, M %A Abril, Josep F %A Guigó, Roderic %A Smit, Arian %A Dubchak, Inna %A Rubin, Edward M %A Couronne, Olivier %A Poliakov, Alexander %A Hübner, Norbert %A Ganten, Detlev %A Goesele, Claudia %A Hummel, Oliver %A Kreitler, Thomas %A Lee, Young-Ae %A Monti, Jan %A Schulz, Herbert %A Zimdahl, Heike %A Himmelbauer, Heinz %A Lehrach, Hans %A Jacob, Howard J %A Bromberg, Susan %A Gullings-Handley, Jo %A Jensen-Seaman, Michael I %A Kwitek, Anne E %A Lazar, Jozef %A Pasko, Dean %A Tonellato, Peter J %A Twigger, Simon %A Ponting, Chris P %A Duarte, Jose M %A Rice, Stephen %A Goodstadt, Leo %A Beatson, Scott A %A Emes, Richard D %A Winter, Eitan E %A Webber, Caleb %A Brandt, Petra %A Nyakatura, Gerald %A Adetobi, Margaret %A Chiaromonte, Francesca %A Elnitski, Laura %A Eswara, Pallavi %A Hardison, Ross C %A Hou, Minmei %A Kolbe, Diana %A Makova, Kateryna %A Miller, Webb %A Nekrutenko, Anton %A Riemer, Cathy %A Schwartz, Scott %A Taylor, James %A Yang, Shan %A Zhang, Yi %A Lindpaintner, Klaus %A Andrews, T Dan %A Caccamo, Mario %A Clamp, Michele %A Clarke, Laura %A Curwen, Valerie %A Durbin, Richard %A Eyras, Eduardo %A Searle, Stephen M %A Cooper, Gregory M %A Batzoglou, Serafim %A Brudno, Michael %A Sidow, Arend %A Stone, Eric A %A Venter, J Craig %A Payseur, Bret A %A Bourque, Guillaume %A López-Otín, Carlos %A Puente, Xose S %A Chakrabarti, Kushal %A Chatterji, Sourav %A Dewey, Colin %A Pachter, Lior %A Bray, Nicolas %A Yap, Von Bing %A Caspi, Anat %A Tesler, Glenn %A Pevzner, Pavel A %A Haussler, David %A Roskin, Krishna M %A Baertsch, Robert %A Clawson, Hiram %A Furey, Terrence S %A Hinrichs, Angie S %A Karolchik, Donna %A Kent, William J %A Rosenbloom, Kate R %A Trumbower, Heather %A Weirauch, Matt %A Cooper, David N %A Stenson, Peter D %A Ma, Bin %A Brent, Michael %A Arumugam, Manimozhiyan %A Shteynberg, David %A Copley, Richard R %A Taylor, Martin S %A Riethman, Harold %A Mudunuri, Uma %A Peterson, Jane %A Guyer, Mark %A Felsenfeld, Adam %A Old, Susan %A Mockrin, Stephen %A Collins, Francis %K Animals %K Base Composition %K Centromere %K Chromosomes, Mammalian %K CpG Islands %K DNA Transposable Elements %K DNA, Mitochondrial %K Evolution, Molecular %K Gene Duplication %K Genome %K Genomics %K Humans %K Introns %K Male %K Mice %K Models, Molecular %K Mutagenesis %K Polymorphism, Single Nucleotide %K Rats %K Rats, Inbred BN %K Regulatory Sequences, Nucleic Acid %K Retroelements %K RNA Splice Sites %K RNA, Untranslated %K Sequence Analysis, DNA %K Telomere %X

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

%B Nature %V 428 %P 493-521 %8 2004 Apr 01 %G eng %N 6982 %1 https://www.ncbi.nlm.nih.gov/pubmed/15057822?dopt=Abstract %R 10.1038/nature02426 %0 Journal Article %J Nature %D 2002 %T Initial sequencing and comparative analysis of the mouse genome. %A Waterston, Robert H %A Lindblad-Toh, Kerstin %A Birney, Ewan %A Rogers, Jane %A Abril, Josep F %A Agarwal, Pankaj %A Agarwala, Richa %A Ainscough, Rachel %A Alexandersson, Marina %A An, Peter %A Antonarakis, Stylianos E %A Attwood, John %A Baertsch, Robert %A Bailey, Jonathon %A Barlow, Karen %A Beck, Stephan %A Berry, Eric %A Birren, Bruce %A Bloom, Toby %A Bork, Peer %A Botcherby, Marc %A Bray, Nicolas %A Brent, Michael R %A Brown, Daniel G %A Brown, Stephen D %A Bult, Carol %A Burton, John %A Butler, Jonathan %A Campbell, Robert D %A Carninci, Piero %A Cawley, Simon %A Chiaromonte, Francesca %A Chinwalla, Asif T %A Church, Deanna M %A Clamp, Michele %A Clee, Christopher %A Collins, Francis S %A Cook, Lisa L %A Copley, Richard R %A Coulson, Alan %A Couronne, Olivier %A Cuff, James %A Curwen, Val %A Cutts, Tim %A Daly, Mark %A David, Robert %A Davies, Joy %A Delehaunty, Kimberly D %A Deri, Justin %A Dermitzakis, Emmanouil T %A Dewey, Colin %A Dickens, Nicholas J %A Diekhans, Mark %A Dodge, Sheila %A Dubchak, Inna %A Dunn, Diane M %A Eddy, Sean R %A Elnitski, Laura %A Emes, Richard D %A Eswara, Pallavi %A Eyras, Eduardo %A Felsenfeld, Adam %A Fewell, Ginger A %A Flicek, Paul %A Foley, Karen %A Frankel, Wayne N %A Fulton, Lucinda A %A Fulton, Robert S %A Furey, Terrence S %A Gage, Diane %A Gibbs, Richard A %A Glusman, Gustavo %A Gnerre, Sante %A Goldman, Nick %A Goodstadt, Leo %A Grafham, Darren %A Graves, Tina A %A Green, Eric D %A Gregory, Simon %A Guigó, Roderic %A Guyer, Mark %A Hardison, Ross C %A Haussler, David %A Hayashizaki, Yoshihide %A Hillier, LaDeana W %A Hinrichs, Angela %A Hlavina, Wratko %A Holzer, Timothy %A Hsu, Fan %A Hua, Axin %A Hubbard, Tim %A Hunt, Adrienne %A Jackson, Ian %A Jaffe, David B %A Johnson, L Steven %A Jones, Matthew %A Jones, Thomas A %A Joy, Ann %A Kamal, Michael %A Karlsson, Elinor K %A Karolchik, Donna %A Kasprzyk, Arkadiusz %A Kawai, Jun %A Keibler, Evan %A Kells, Cristyn %A Kent, W James %A Kirby, Andrew %A Kolbe, Diana L %A Korf, Ian %A Kucherlapati, Raju S %A Kulbokas, Edward J %A Kulp, David %A Landers, Tom %A Leger, J P %A Leonard, Steven %A Letunic, Ivica %A Levine, Rosie %A Li, Jia %A Li, Ming %A Lloyd, Christine %A Lucas, Susan %A Ma, Bin %A Maglott, Donna R %A Mardis, Elaine R %A Matthews, Lucy %A Mauceli, Evan %A Mayer, John H %A McCarthy, Megan %A McCombie, W Richard %A McLaren, Stuart %A McLay, Kirsten %A McPherson, John D %A Meldrim, Jim %A Meredith, Beverley %A Mesirov, Jill P %A Miller, Webb %A Miner, Tracie L %A Mongin, Emmanuel %A Montgomery, Kate T %A Morgan, Michael %A Mott, Richard %A Mullikin, James C %A Muzny, Donna M %A Nash, William E %A Nelson, Joanne O %A Nhan, Michael N %A Nicol, Robert %A Ning, Zemin %A Nusbaum, Chad %A O'Connor, Michael J %A Okazaki, Yasushi %A Oliver, Karen %A Overton-Larty, Emma %A Pachter, Lior %A Parra, Genís %A Pepin, Kymberlie H %A Peterson, Jane %A Pevzner, Pavel %A Plumb, Robert %A Pohl, Craig S %A Poliakov, Alex %A Ponce, Tracy C %A Ponting, Chris P %A Potter, Simon %A Quail, Michael %A Reymond, Alexandre %A Roe, Bruce A %A Roskin, Krishna M %A Rubin, Edward M %A Rust, Alistair G %A Santos, Ralph %A Sapojnikov, Victor %A Schultz, Brian %A Schultz, Jörg %A Schwartz, Matthias S %A Schwartz, Scott %A Scott, Carol %A Seaman, Steven %A Searle, Steve %A Sharpe, Ted %A Sheridan, Andrew %A Shownkeen, Ratna %A Sims, Sarah %A Singer, Jonathan B %A Slater, Guy %A Smit, Arian %A Smith, Douglas R %A Spencer, Brian %A Stabenau, Arne %A Stange-Thomann, Nicole %A Sugnet, Charles %A Suyama, Mikita %A Tesler, Glenn %A Thompson, Johanna %A Torrents, David %A Trevaskis, Evanne %A Tromp, John %A Ucla, Catherine %A Ureta-Vidal, Abel %A Vinson, Jade P %A Von Niederhausern, Andrew C %A Wade, Claire M %A Wall, Melanie %A Weber, Ryan J %A Weiss, Robert B %A Wendl, Michael C %A West, Anthony P %A Wetterstrand, Kris %A Wheeler, Raymond %A Whelan, Simon %A Wierzbowski, Jamey %A Willey, David %A Williams, Sophie %A Wilson, Richard K %A Winter, Eitan %A Worley, Kim C %A Wyman, Dudley %A Yang, Shan %A Yang, Shiaw-Pyng %A Zdobnov, Evgeny M %A Zody, Michael C %A Lander, Eric S %K Animals %K Base Composition %K Chromosomes, Mammalian %K Conserved Sequence %K CpG Islands %K Evolution, Molecular %K Gene Expression Regulation %K Genes %K Genetic Variation %K Genome %K Genome, Human %K Genomics %K Humans %K Mice %K Mice, Knockout %K Mice, Transgenic %K Models, Animal %K Multigene Family %K Mutagenesis %K Neoplasms %K Physical Chromosome Mapping %K Proteome %K Pseudogenes %K Quantitative Trait Loci %K Repetitive Sequences, Nucleic Acid %K RNA, Untranslated %K Selection, Genetic %K Sequence Analysis, DNA %K Sex Chromosomes %K Species Specificity %K Synteny %X

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

%B Nature %V 420 %P 520-62 %8 2002 Dec 05 %G eng %N 6915 %1 https://www.ncbi.nlm.nih.gov/pubmed/12466850?dopt=Abstract %R 10.1038/nature01262